Variant report

Variant	rs962399
Chromosome Location	chr4:103308907-103308908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103308466..103311400-chr4:103313181..103314983,2	MCF-7	breast:
2	chr4:103307851..103309753-chr4:103332388..103335045,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10008684	0.81[EUR][1000 genomes]
rs10019247	0.86[EUR][1000 genomes]
rs10461136	0.90[EUR][1000 genomes]
rs10516492	0.84[ASN][1000 genomes]
rs10516493	0.84[ASN][1000 genomes]
rs11097775	0.87[ASN][1000 genomes]
rs11097776	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097777	0.85[ASN][1000 genomes]
rs11097779	0.86[ASN][1000 genomes]
rs11097780	0.88[EUR][1000 genomes]
rs1117520	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap]
rs1117522	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1159788	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11728286	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730379	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730944	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730958	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11935847	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12499248	0.95[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs12500141	0.87[EUR][1000 genomes]
rs12505568	0.86[EUR][1000 genomes]
rs12508086	0.85[ASN][1000 genomes]
rs12508121	0.85[ASN][1000 genomes]
rs12510124	0.87[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs13104988	0.86[EUR][1000 genomes]
rs13107285	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13112930	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13114804	0.88[EUR][1000 genomes]
rs13125848	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13147260	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1381893	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs1381894	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1381895	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1381897	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1381899	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462943	0.91[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs1462945	0.85[ASN][1000 genomes]
rs1462948	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462949	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462950	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462951	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1462952	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1599684	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1599685	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1599686	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17032552	0.87[ASN][1000 genomes]
rs1870952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054393	0.91[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs2086004	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2126625	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34197129	0.89[JPT][hapmap]
rs34835832	0.95[EUR][1000 genomes]
rs34927061	0.84[ASN][1000 genomes]
rs35651507	0.84[ASN][1000 genomes]
rs4146611	0.87[ASN][1000 genomes]
rs4356914	0.87[ASN][1000 genomes]
rs4594728	0.87[ASN][1000 genomes]
rs4699012	0.80[CHD][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap]
rs4699019	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699020	0.87[ASN][1000 genomes]
rs4699021	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699024	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699026	0.82[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs55801262	0.86[ASN][1000 genomes]
rs56202913	0.84[ASN][1000 genomes]
rs56344531	0.86[ASN][1000 genomes]
rs62328212	0.87[ASN][1000 genomes]
rs6533014	0.83[GIH][hapmap]
rs6810692	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6814302	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6835467	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843751	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6844796	0.90[EUR][1000 genomes]
rs6856314	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7436937	0.87[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs7657947	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661593	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7683109	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7695249	0.87[ASN][1000 genomes]
rs984055	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996947	0.89[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs962399	GSTCD	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103306600-103309000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:103307400-103309000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:103308000-103312800	Weak transcription	Placenta	Placenta
4	chr4:103308600-103309800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:103308800-103309000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:103308800-103309400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:103308800-103310200	Enhancers	Hela-S3	cervix
8	chr4:103308800-103312400	Enhancers	HMEC	breast

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